Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae)

Abstract

Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species’ genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species’ 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.

The Genetic Basis of Tomato Aroma

“…These techniques include over a dozen of reduced-representation sequencing (RRS) approaches [39] and have been recently applied for high-resolution QTL mapping in tomato, especially in interspecific crosses [40][41][42][43]. These protocols have been applied in the development of high-density genetic maps in many different species [44][45][46][47][48][49][50][51][52][53][54][55], making it possible to perform comparative and quantitative genetics in virtually any genomic background. The current advances in genome sequencing technologies, such as a revolutionary increase of sequencing throughput and concomitant reduction in costs per sequenced nucleotide, allowed to unravel the genetic variation in tomato to its full extent [25,56,57] and has helped to realize that the concept of one or a few reference genomes is not sufficient to fully understand the genetic control of traits.…”

Toward the Genetic Improvement of Drought Tolerance in Conifers: An Integrated Approach

“…A complete list of genomic resources of conifers, with the year of release, the Genebank storage and the accession number, has been reported by Traversari et al [194]. These data, together with transcriptome studies, have provided useful information for the development of high-density genetic maps [195][196][197][198][199] and SNP arrays [200][201][202][203][204], which could be used in next-generation breeding approaches. To date, marker-assisted selection (MAS) has shown only a limited application in forest breeding [205,206].…”